Former Jemaah Islamiah bomb expert Taufik Abdul Halim was among 350 former Jemaah Islamiah members released from Indonesian prisons after being granted a pardon from President Joko Widodo.

Jemaah Islamiyah (JI) bomb-maker, Taufik Abdul Halim alias Dany (pic), 39, returned to Malaysia last week after spending 12 years in an Indonesian prison for his involvement in a blast in a Jakarta mall where he ended up losing his right leg when the home-made explosives exploded early.

While in prison, one of Southeast Asia's most wanted militant with a US$5mil (S$6.5mil) bounty on his head, his brother-in-law, Zulkifli Abdul Khir, also known as Marwan, managed to make contact with him, according to regional security officials.

Marwan is believed to be hiding in the southern Philippines where security officials say he is training members of the militant Abu Sayyaf Group (ASG) on how to assemble bombs.

"Marwan contacted Taufik when he was in prison," a regional counter-terrorism official told The Star, without giving details.

According to Indonesian counter-terrorism sources, it is very difficult to control and monitor activities of militants in prison due to over-crowding.

Most Indonesian prisons are built to accommodate 1,000 inmates but many of them hold an average of 2,500.

"There are so many people in jail and it is very difficult to monitor all the activities of militants.

"It is possible that someone lent Dany a phone or he could have borrowed one while in prison," a source told The Star.

Communications between Mar­wan and Dany underscores the sophistication in which militants keep in touch and circumvent the prison system in Indonesia.

Last year, overcrowding in the Tanjung Gusta prison in Indonesia's city of Medan erupted into a riot, resulting in the death of three inmates and two prison personnel.

During the melee, at least 218 inmates escaped, including convicted terrorists. Most of them have since been re-arrested.

Prison was also the place where JI's spiritual leader, Abu Bakar Bashir, introduced Dany to his Indonesian wife. Bashir, 76, is currently serving a 15-year jail sentence for terrorism offences.

"They have an eight-year-old child.

"Dany returned home to Malay­sia together with his Indonesian wife and the child," a Malaysian counter-terrorism official said.

Dany is currently in his family home in Kluang, Johor.

An official of the Malay­sian Embassy who used to visit Dany in prison between 2003 and 2006, described him as a "soft-spoken man" who was "depressed over losing his leg".

"During one of the visits, he told me "nobody likes me".

He was also depressed about losing his limb and talked about missing his loved ones back home," said the embassy official.

"I told Dany to write a book about his life, to give lessons to others and that would be a good repentance in the eyes of God.

I don't know whether he ever wrote that book,"

"I believe he was quite well-treated in prison as he never once complained or made any request for anything even though I told him to let me know if he needed anything," said the official.

The official said the authorities should not leave Dany to his own devices and should engage with him through a de-radicalisation programme.

"We have to help him re-integrate back into society and let him find a way to earn a living," the official said.

Dany was initially sentenced to death for his role in the 2001 Jakarta blast at Plaza Atrium Senen.

The sentence was later commuted to a prison term.

The bomb was meant to be planted on a bus, parked next to the mall, which was used to transport Christians. However, it went off while Dany was carrying it.

Dany was also involved in the bombing of two churches in east Jakarta that same year.

Prior to Jakarta, Dany went to wage war against Christians in Indonesia's Maluku islands in 2000 where fighting erupted between Muslims and Christians from 1999-2002.

Because of his bomb-making skills and his links with Marwan, Malaysian police are expected to closely monitor his activities.

"He is not involved in any militant activities now. You can take the militant activities away from him. But the ideology remains and it takes time to remove it," said the Malaysian counter-terrorism official.

Dany was detained between October and November 1996 under the Internal Security Act (ISA) when he returned from Pakistan and Afghanistan where he had undergone para-military training.

His brother-in-law, Marwan, is regarded as "dangerous" and is believed to be an expert bomb-maker.

According to the FBI website, Marwan is thought to be the head of the militant Kumpulan Mujahidin Malaysia (KMM) terrorist organisation and a member of JI's central command.

Marwan is an engineer trained in the United States. It is believed that he has been living in the Southern Philippines since August 2003.